CT Phipps
Carbon Dated and Proud

You have to follow the same basic plot of Pre-War, finding relative, Commonwealth, and the factions but you can mix it up otherwise.
How would you do it?
Here's my ideas.
C.T. Phipps' Fallout 4
0. Stick with the SPECIAL system rather than reinventing it. Keep options of story relevance and incorporate skills into the game.
1. The Sole Survivor is the brother/sister of Nora rather than the husband. Hence, Shaun is the Sole Survivor's nephew and they have much more freedom to choose what their identity was in the Pre-War world. You can claim to be a variety of professions or just refuse to talk about them and be mysterious. There'd be about 30 minutes in the starting area where you'd have to deal with youth gangs trying to steal your car's microfusion battery, talk about how you can only eat sugar pops, and also dealing with a power armored soldier who is threatening the two women across the street. Nora signed you both up at Vault-Tech. When you flee to the Vault, you see the nuclear explosion on monitors in the Vault.
2. I'd make the opening Vault area far more gruesome as you wake up to find the entire place full of skeletons rather than frozen people with only the barest of power. Your sister's pod is empty, however, and you are on a mystery which will be to find out what happened to them rather than "who killed them." The game will emphasize you have almost no clues whatsoever so it's not something meant to drive the plot as closure to the end.
3. At the start of the game you'll have the option of choosing to side with either the Minutemen or the Nuka World Raiders. The latter will be fully integrated into the game with backstories, histories, bases, and the option of communicating with them. You'll also be able to sneak the survivors out of the area or just bribe or speech the Nuka World Raiders into leaving them alone. I.e. You can keep from making one into your enemy at the start. MacCready is the Raider Companion and Preston is the Minuteman Companion, no exceptions.
4. The Institute is actually a walled Vault City-esque location inside the Commonwealth without much difficulty getting in. It's a picturesque Utopia that is run by robotic slave labor. The Institute considers the surrounding people of the Commonwealth to be primitive savages and sends out Synths to infiltrate the other groups to keep them from trying to attack the Institute in order to steal their stuff. You need a pass to get into the Institute which you can do by forging one, rescuing some Institute scavengers, or just showing enough skills at Science or Medicine to get in.
5. Arthur Maxson has returned the BoS to its original goal of stealing technology. The Institute has to go because it is a collection of advanced technology which "threatens the world." I don't try and make that sympathetic. The Institute and BoS are irreconciable as long as he's in charge. On the other hand, I do highlight the BOS has changed under Maxson to being a feudal state that they actively rule territories under their control now. They control the Capital Wasteland and Arthur envisions eventually building a Brotherhood Empire.
A major plotlline is discovering that Scribe Rothschild arranged for Arthur to replace Sarah Lyons and have the Lone Wanderer exiled from the Brotherhood to return to a traditionalist Brotherhood. You can find Sarah Lyon's body and audiodiaries that prove the treachery. You can then decide to have Rothschild executed, destroy the evidence, replace Maxson with Danse (you lose him as a companion as a result), or use it to influence Maxson.
Eliminate the whole Danse is a Synth thing.
6. The Railroad isn't an actual faction in this game but just a spin-off of the Institute. They're a bunch of exiled citizens that either fell in love with their Synths or committed some crime against the Institute. They're a minor faction but a useful faction which just helps broaden the organization as a whole.
7. Massively pair down the Settlement system. There's four Settlements in the entire game with your initial settlement in Santuary Hills, Lookout Point, the Fortress, and making your home base at the Rockets. It's a side-game and largely irrelevant to the system.
8. The Final Battle in the game is either an attack on the Institute for its many crimes by the Raiders or Brotherhood of Steel or defending the Institute. You can have the Minutemen either assist the Brotherhood of Steel or the Brotherhood of Steel in attacking the location. The final battle will include many people showing up who you helped or not similar to the Battle of Hoover Dam. You can also actually totally subvert the typical Fallout business by forcing a peace treaty between the factions through a complicated questline and speech.
The final boss will be Liberty Prime for the BOS (which you can sabotage beforehand so he doesn't do anything or explodes) or a Institute mecha.
9. Tweak the lore so it's actually consistent. The Institute has its own unique brand of Power Armor they created post-apocalypse. The Super Mutants in the Commonwealth are survivors of Washington D.C. driven North by them after having their base destroyed by the boS/Lone Wanderer. No references to Jet before the apocalypse.
Yes, this means either Codsworth and Curie are RoboBrains or they don't exist.
10. Generally expand the amount of things to do and say without shooting things. Adding in the Racetrack for Robots, the Combat Zone, the option to get married, the chance to join the Church of the Atom, and on is all there to make the place feel more authentic. There should also be a good deal better voice options with at least some consistency and knowing what you're saying.
11. As for Shaun? You actually find out the Institute shut down the power of your Vault to steal it. Kellog, however, had a moment of humanity and refused to kill a woman with a baby. She also insisted on leaving her brother alive. You have learn Kellog's history via the Memory Reader to track him down (he's a frequent user) and find this out. You can spare him or not but if you do, he becomes a companion. Later, you'll find your sister is an old woman now living with the Railroad while Shaun is an Institute scientist but not Father.
12. Obviously, we keep the "What happens to X" slideshow.
How would you do it?
Here's my ideas.
C.T. Phipps' Fallout 4
0. Stick with the SPECIAL system rather than reinventing it. Keep options of story relevance and incorporate skills into the game.
1. The Sole Survivor is the brother/sister of Nora rather than the husband. Hence, Shaun is the Sole Survivor's nephew and they have much more freedom to choose what their identity was in the Pre-War world. You can claim to be a variety of professions or just refuse to talk about them and be mysterious. There'd be about 30 minutes in the starting area where you'd have to deal with youth gangs trying to steal your car's microfusion battery, talk about how you can only eat sugar pops, and also dealing with a power armored soldier who is threatening the two women across the street. Nora signed you both up at Vault-Tech. When you flee to the Vault, you see the nuclear explosion on monitors in the Vault.
2. I'd make the opening Vault area far more gruesome as you wake up to find the entire place full of skeletons rather than frozen people with only the barest of power. Your sister's pod is empty, however, and you are on a mystery which will be to find out what happened to them rather than "who killed them." The game will emphasize you have almost no clues whatsoever so it's not something meant to drive the plot as closure to the end.
3. At the start of the game you'll have the option of choosing to side with either the Minutemen or the Nuka World Raiders. The latter will be fully integrated into the game with backstories, histories, bases, and the option of communicating with them. You'll also be able to sneak the survivors out of the area or just bribe or speech the Nuka World Raiders into leaving them alone. I.e. You can keep from making one into your enemy at the start. MacCready is the Raider Companion and Preston is the Minuteman Companion, no exceptions.
4. The Institute is actually a walled Vault City-esque location inside the Commonwealth without much difficulty getting in. It's a picturesque Utopia that is run by robotic slave labor. The Institute considers the surrounding people of the Commonwealth to be primitive savages and sends out Synths to infiltrate the other groups to keep them from trying to attack the Institute in order to steal their stuff. You need a pass to get into the Institute which you can do by forging one, rescuing some Institute scavengers, or just showing enough skills at Science or Medicine to get in.
5. Arthur Maxson has returned the BoS to its original goal of stealing technology. The Institute has to go because it is a collection of advanced technology which "threatens the world." I don't try and make that sympathetic. The Institute and BoS are irreconciable as long as he's in charge. On the other hand, I do highlight the BOS has changed under Maxson to being a feudal state that they actively rule territories under their control now. They control the Capital Wasteland and Arthur envisions eventually building a Brotherhood Empire.
A major plotlline is discovering that Scribe Rothschild arranged for Arthur to replace Sarah Lyons and have the Lone Wanderer exiled from the Brotherhood to return to a traditionalist Brotherhood. You can find Sarah Lyon's body and audiodiaries that prove the treachery. You can then decide to have Rothschild executed, destroy the evidence, replace Maxson with Danse (you lose him as a companion as a result), or use it to influence Maxson.
Eliminate the whole Danse is a Synth thing.
6. The Railroad isn't an actual faction in this game but just a spin-off of the Institute. They're a bunch of exiled citizens that either fell in love with their Synths or committed some crime against the Institute. They're a minor faction but a useful faction which just helps broaden the organization as a whole.
7. Massively pair down the Settlement system. There's four Settlements in the entire game with your initial settlement in Santuary Hills, Lookout Point, the Fortress, and making your home base at the Rockets. It's a side-game and largely irrelevant to the system.
8. The Final Battle in the game is either an attack on the Institute for its many crimes by the Raiders or Brotherhood of Steel or defending the Institute. You can have the Minutemen either assist the Brotherhood of Steel or the Brotherhood of Steel in attacking the location. The final battle will include many people showing up who you helped or not similar to the Battle of Hoover Dam. You can also actually totally subvert the typical Fallout business by forcing a peace treaty between the factions through a complicated questline and speech.
The final boss will be Liberty Prime for the BOS (which you can sabotage beforehand so he doesn't do anything or explodes) or a Institute mecha.
9. Tweak the lore so it's actually consistent. The Institute has its own unique brand of Power Armor they created post-apocalypse. The Super Mutants in the Commonwealth are survivors of Washington D.C. driven North by them after having their base destroyed by the boS/Lone Wanderer. No references to Jet before the apocalypse.
Yes, this means either Codsworth and Curie are RoboBrains or they don't exist.
10. Generally expand the amount of things to do and say without shooting things. Adding in the Racetrack for Robots, the Combat Zone, the option to get married, the chance to join the Church of the Atom, and on is all there to make the place feel more authentic. There should also be a good deal better voice options with at least some consistency and knowing what you're saying.
11. As for Shaun? You actually find out the Institute shut down the power of your Vault to steal it. Kellog, however, had a moment of humanity and refused to kill a woman with a baby. She also insisted on leaving her brother alive. You have learn Kellog's history via the Memory Reader to track him down (he's a frequent user) and find this out. You can spare him or not but if you do, he becomes a companion. Later, you'll find your sister is an old woman now living with the Railroad while Shaun is an Institute scientist but not Father.
12. Obviously, we keep the "What happens to X" slideshow.